Multiple sequence alignment - TraesCS5D01G547300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G547300 chr5D 100.000 3302 0 0 1 3302 555500646 555503947 0.000000e+00 6098.0
1 TraesCS5D01G547300 chr5D 91.248 2628 215 7 679 3302 555062190 555064806 0.000000e+00 3565.0
2 TraesCS5D01G547300 chr5D 88.460 2331 226 21 607 2910 555045932 555048246 0.000000e+00 2774.0
3 TraesCS5D01G547300 chr5D 78.649 2590 505 37 730 3299 555635854 555638415 0.000000e+00 1676.0
4 TraesCS5D01G547300 chr5D 77.015 2593 543 46 733 3302 495551815 495549253 0.000000e+00 1437.0
5 TraesCS5D01G547300 chr5D 76.412 2603 565 40 722 3302 464701193 464698618 0.000000e+00 1360.0
6 TraesCS5D01G547300 chr5D 76.572 2386 516 33 925 3294 555356792 555359150 0.000000e+00 1269.0
7 TraesCS5D01G547300 chr5D 78.740 1444 283 19 1867 3302 555488354 555489781 0.000000e+00 944.0
8 TraesCS5D01G547300 chr5D 87.338 616 46 15 4 611 555061513 555062104 0.000000e+00 676.0
9 TraesCS5D01G547300 chr5D 91.411 326 28 0 2977 3302 555048244 555048569 6.500000e-122 448.0
10 TraesCS5D01G547300 chr5D 93.333 60 4 0 607 666 555062142 555062201 4.540000e-14 89.8
11 TraesCS5D01G547300 chr5B 77.898 2588 526 38 734 3302 695493864 695491304 0.000000e+00 1568.0
12 TraesCS5D01G547300 chr5B 78.900 1109 214 14 2200 3302 695875784 695874690 0.000000e+00 734.0
13 TraesCS5D01G547300 chr5A 75.679 2578 588 30 737 3297 585201877 585199322 0.000000e+00 1251.0
14 TraesCS5D01G547300 chr6A 75.814 1935 417 40 869 2780 11233980 11235886 0.000000e+00 933.0
15 TraesCS5D01G547300 chr2B 71.877 1657 406 50 1672 3302 779882385 779880763 1.100000e-114 424.0
16 TraesCS5D01G547300 chr1B 81.053 285 43 7 733 1013 433644762 433644485 2.000000e-52 217.0
17 TraesCS5D01G547300 chr7D 81.169 154 29 0 807 960 28035032 28035185 1.240000e-24 124.0
18 TraesCS5D01G547300 chr7A 74.818 274 62 7 807 1077 28453852 28454121 2.080000e-22 117.0
19 TraesCS5D01G547300 chr4A 86.170 94 13 0 867 960 701757206 701757299 5.830000e-18 102.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G547300 chr5D 555500646 555503947 3301 False 6098.0 6098 100.000000 1 3302 1 chr5D.!!$F3 3301
1 TraesCS5D01G547300 chr5D 555635854 555638415 2561 False 1676.0 1676 78.649000 730 3299 1 chr5D.!!$F4 2569
2 TraesCS5D01G547300 chr5D 555045932 555048569 2637 False 1611.0 2774 89.935500 607 3302 2 chr5D.!!$F5 2695
3 TraesCS5D01G547300 chr5D 555061513 555064806 3293 False 1443.6 3565 90.639667 4 3302 3 chr5D.!!$F6 3298
4 TraesCS5D01G547300 chr5D 495549253 495551815 2562 True 1437.0 1437 77.015000 733 3302 1 chr5D.!!$R2 2569
5 TraesCS5D01G547300 chr5D 464698618 464701193 2575 True 1360.0 1360 76.412000 722 3302 1 chr5D.!!$R1 2580
6 TraesCS5D01G547300 chr5D 555356792 555359150 2358 False 1269.0 1269 76.572000 925 3294 1 chr5D.!!$F1 2369
7 TraesCS5D01G547300 chr5D 555488354 555489781 1427 False 944.0 944 78.740000 1867 3302 1 chr5D.!!$F2 1435
8 TraesCS5D01G547300 chr5B 695491304 695493864 2560 True 1568.0 1568 77.898000 734 3302 1 chr5B.!!$R1 2568
9 TraesCS5D01G547300 chr5B 695874690 695875784 1094 True 734.0 734 78.900000 2200 3302 1 chr5B.!!$R2 1102
10 TraesCS5D01G547300 chr5A 585199322 585201877 2555 True 1251.0 1251 75.679000 737 3297 1 chr5A.!!$R1 2560
11 TraesCS5D01G547300 chr6A 11233980 11235886 1906 False 933.0 933 75.814000 869 2780 1 chr6A.!!$F1 1911
12 TraesCS5D01G547300 chr2B 779880763 779882385 1622 True 424.0 424 71.877000 1672 3302 1 chr2B.!!$R1 1630

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
516 524 0.250901 AGTGGCAAAGCTGGTGTAGG 60.251 55.0 0.0 0.0 0.0 3.18 F
876 953 0.308684 CGCTGCTCACTTTCAAAGCA 59.691 50.0 0.0 0.0 43.4 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2323 1.270550 GGGCTCAGTGAATTGGTTGTG 59.729 52.381 0.00 0.0 0.0 3.33 R
2832 2915 1.139058 CGGTATTTGGCCTGCTAGACT 59.861 52.381 3.32 0.0 0.0 3.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 4.118093 TCATTTTGATGCAATGCAGAGG 57.882 40.909 14.98 0.00 43.65 3.69
49 50 2.373540 TTTTGATGCAATGCAGAGGC 57.626 45.000 14.98 3.74 43.65 4.70
60 62 2.829592 CAGAGGCCGGGGTAATCC 59.170 66.667 2.18 0.00 0.00 3.01
62 64 1.766461 AGAGGCCGGGGTAATCCTG 60.766 63.158 2.18 0.00 41.69 3.86
63 65 2.042261 AGGCCGGGGTAATCCTGT 59.958 61.111 2.18 0.00 40.38 4.00
67 69 1.100510 GCCGGGGTAATCCTGTTTTC 58.899 55.000 2.18 0.00 40.38 2.29
68 70 1.340697 GCCGGGGTAATCCTGTTTTCT 60.341 52.381 2.18 0.00 40.38 2.52
69 71 2.882643 GCCGGGGTAATCCTGTTTTCTT 60.883 50.000 2.18 0.00 40.38 2.52
111 113 0.776451 GCTATACGGACGACAATGCG 59.224 55.000 0.00 0.00 39.62 4.73
127 129 1.007038 GCGTGTACGGTGAACAGGA 60.007 57.895 6.55 0.00 40.23 3.86
128 130 0.598158 GCGTGTACGGTGAACAGGAA 60.598 55.000 6.55 0.00 40.23 3.36
129 131 1.855513 CGTGTACGGTGAACAGGAAA 58.144 50.000 0.00 0.00 35.31 3.13
130 132 1.523934 CGTGTACGGTGAACAGGAAAC 59.476 52.381 0.00 0.00 35.31 2.78
133 135 3.985925 GTGTACGGTGAACAGGAAACTAG 59.014 47.826 0.00 0.00 40.21 2.57
134 136 3.890756 TGTACGGTGAACAGGAAACTAGA 59.109 43.478 0.00 0.00 40.21 2.43
135 137 4.341806 TGTACGGTGAACAGGAAACTAGAA 59.658 41.667 0.00 0.00 40.21 2.10
136 138 4.618920 ACGGTGAACAGGAAACTAGAAT 57.381 40.909 0.00 0.00 40.21 2.40
137 139 4.566987 ACGGTGAACAGGAAACTAGAATC 58.433 43.478 0.00 0.00 40.21 2.52
138 140 3.612860 CGGTGAACAGGAAACTAGAATCG 59.387 47.826 0.00 0.00 40.21 3.34
139 141 4.566987 GGTGAACAGGAAACTAGAATCGT 58.433 43.478 0.00 0.00 40.21 3.73
140 142 4.389077 GGTGAACAGGAAACTAGAATCGTG 59.611 45.833 15.59 15.59 40.21 4.35
182 184 2.124570 CCCATGGACCTTCTGCCG 60.125 66.667 15.22 0.00 0.00 5.69
211 213 1.003355 AACGGATGCTGGTCAGTGG 60.003 57.895 0.00 0.00 0.00 4.00
241 243 3.393089 AGAAGGCGGCAGTATCTAATG 57.607 47.619 13.08 0.00 0.00 1.90
244 246 3.113260 AGGCGGCAGTATCTAATGTTC 57.887 47.619 13.08 0.00 0.00 3.18
256 258 8.554528 CAGTATCTAATGTTCCTGCACTTAATG 58.445 37.037 0.00 0.00 0.00 1.90
264 272 1.860950 CCTGCACTTAATGATCGACGG 59.139 52.381 0.00 0.00 0.00 4.79
266 274 1.286501 GCACTTAATGATCGACGGCA 58.713 50.000 0.00 0.00 0.00 5.69
288 296 3.919216 AGTCTAGCTAGTTGCACAGTTG 58.081 45.455 20.10 0.00 45.94 3.16
296 304 2.663826 GTTGCACAGTTGGAACCAAA 57.336 45.000 7.89 0.00 45.74 3.28
297 305 3.177997 GTTGCACAGTTGGAACCAAAT 57.822 42.857 7.89 4.21 45.74 2.32
298 306 3.530535 GTTGCACAGTTGGAACCAAATT 58.469 40.909 7.89 0.00 45.74 1.82
299 307 3.451141 TGCACAGTTGGAACCAAATTC 57.549 42.857 7.89 0.00 37.70 2.17
300 308 2.762887 TGCACAGTTGGAACCAAATTCA 59.237 40.909 7.89 2.79 39.30 2.57
301 309 3.387374 TGCACAGTTGGAACCAAATTCAT 59.613 39.130 7.89 0.00 39.30 2.57
302 310 3.989817 GCACAGTTGGAACCAAATTCATC 59.010 43.478 7.89 0.00 39.30 2.92
303 311 4.501229 GCACAGTTGGAACCAAATTCATCA 60.501 41.667 7.89 0.00 39.30 3.07
309 317 7.329226 CAGTTGGAACCAAATTCATCAATACAC 59.671 37.037 7.89 0.00 39.30 2.90
423 431 4.811024 TCAGCATTTTGTTAGATAGCTCCG 59.189 41.667 0.00 0.00 0.00 4.63
443 451 1.017177 GGCCGTGTCGTTATGCTTGA 61.017 55.000 0.00 0.00 0.00 3.02
487 495 1.541147 CCATGGCATTGTCGACAAGTT 59.459 47.619 32.19 16.93 39.47 2.66
489 497 2.772568 TGGCATTGTCGACAAGTTTG 57.227 45.000 32.19 26.11 39.47 2.93
511 519 4.404691 GCTAGTGGCAAAGCTGGT 57.595 55.556 14.14 0.00 41.35 4.00
516 524 0.250901 AGTGGCAAAGCTGGTGTAGG 60.251 55.000 0.00 0.00 0.00 3.18
543 551 1.753848 TCCGCTCCGATCGGGTAAA 60.754 57.895 32.79 13.65 46.43 2.01
545 553 0.666577 CCGCTCCGATCGGGTAAATC 60.667 60.000 32.79 14.47 42.99 2.17
571 579 1.207593 GTGTGGTGCATGTTCGAGC 59.792 57.895 0.00 0.00 0.00 5.03
575 583 1.229975 TGGTGCATGTTCGAGCAGTG 61.230 55.000 8.26 7.57 42.14 3.66
645 695 1.062525 CGCCGGCAAGCTAATTGAC 59.937 57.895 28.98 0.00 44.22 3.18
666 716 0.953727 GATGCACTTGTGGCACAGAA 59.046 50.000 20.97 6.10 45.23 3.02
674 724 3.706086 ACTTGTGGCACAGAAAAAGGATT 59.294 39.130 20.97 0.00 42.33 3.01
677 727 4.724399 TGTGGCACAGAAAAAGGATTAGA 58.276 39.130 17.96 0.00 41.80 2.10
680 730 6.095377 GTGGCACAGAAAAAGGATTAGATTG 58.905 40.000 13.86 0.00 41.80 2.67
709 759 2.172717 AGCCCATATAAACTCACCGCTT 59.827 45.455 0.00 0.00 0.00 4.68
731 802 2.487086 CCCTTGATGTTCACTCCACACA 60.487 50.000 0.00 0.00 0.00 3.72
795 869 6.239176 CCATCTTTGTGATAGTCCTACTCTCC 60.239 46.154 0.00 0.00 33.36 3.71
817 891 1.032657 TCTCTCGGCTTCTTCTCCCG 61.033 60.000 0.00 0.00 43.21 5.14
824 898 1.885163 GCTTCTTCTCCCGGTCCGAA 61.885 60.000 14.39 0.00 0.00 4.30
830 907 2.203523 TCCCGGTCCGAACAGTGA 60.204 61.111 14.39 0.00 0.00 3.41
865 942 3.633094 GACCTCGAAGCGCTGCTCA 62.633 63.158 12.58 0.00 38.25 4.26
876 953 0.308684 CGCTGCTCACTTTCAAAGCA 59.691 50.000 0.00 0.00 43.40 3.91
941 1018 1.508632 GGCACGTCTTTCTGCAACTA 58.491 50.000 0.00 0.00 34.90 2.24
1093 1170 3.393426 ACAATCTGATGGGCTCCATTT 57.607 42.857 7.97 0.00 45.26 2.32
1148 1225 8.050778 AGGTATCTCGATCTCATGAGAAATAC 57.949 38.462 28.40 24.24 43.89 1.89
1530 1611 3.255969 TGCGGTAACCTAACTGGAATC 57.744 47.619 0.00 0.00 39.71 2.52
1599 1680 6.632909 TGCAATATCTGGGAACAAATTTGAG 58.367 36.000 24.64 10.92 42.06 3.02
1609 1690 4.442332 GGAACAAATTTGAGGGTCGGTTTT 60.442 41.667 24.64 4.23 0.00 2.43
1643 1724 3.181451 GCATCATGTCAATACCTCCAGGA 60.181 47.826 0.00 0.00 38.94 3.86
1720 1801 9.039870 CCAAATTGTCACAACTAAAAATGCTTA 57.960 29.630 0.00 0.00 0.00 3.09
1872 1953 6.003950 TGAACTCTGGTTTCTTAATCTTGGG 58.996 40.000 0.00 0.00 35.58 4.12
1875 1956 5.548056 ACTCTGGTTTCTTAATCTTGGGAGA 59.452 40.000 0.00 0.00 36.09 3.71
1885 1966 7.775120 TCTTAATCTTGGGAGAAATCAATTGC 58.225 34.615 0.00 0.00 35.07 3.56
1886 1967 7.616935 TCTTAATCTTGGGAGAAATCAATTGCT 59.383 33.333 0.00 0.00 35.07 3.91
1956 2037 9.699410 ATCCTTGGTTTGTCTCATAATCAATTA 57.301 29.630 0.00 0.00 0.00 1.40
1976 2057 2.738587 TCTGGCCAAGTACCAACAAA 57.261 45.000 7.01 0.00 36.56 2.83
2130 2211 1.964933 GGTGTCCTCCCTAGCTATGTC 59.035 57.143 0.00 0.00 0.00 3.06
2169 2250 4.989279 ATTAGACATGTTCATTGCACCC 57.011 40.909 0.00 0.00 0.00 4.61
2225 2306 5.345741 CGATTTCAAACCTAAGCAACATTGG 59.654 40.000 0.00 0.00 0.00 3.16
2235 2316 7.048512 ACCTAAGCAACATTGGTCTAATAGAC 58.951 38.462 11.79 11.79 44.32 2.59
2249 2330 5.027460 TCTAATAGACCTTAGCCACAACCA 58.973 41.667 0.00 0.00 0.00 3.67
2278 2359 1.146566 AGCCCATTCCAGAATCCATCC 59.853 52.381 0.00 0.00 0.00 3.51
2300 2381 6.980593 TCCTTATGTTGGAAAATCTTGTGTG 58.019 36.000 0.00 0.00 0.00 3.82
2301 2382 6.775142 TCCTTATGTTGGAAAATCTTGTGTGA 59.225 34.615 0.00 0.00 0.00 3.58
2302 2383 7.451255 TCCTTATGTTGGAAAATCTTGTGTGAT 59.549 33.333 0.00 0.00 0.00 3.06
2303 2384 7.543172 CCTTATGTTGGAAAATCTTGTGTGATG 59.457 37.037 0.00 0.00 0.00 3.07
2304 2385 5.850557 TGTTGGAAAATCTTGTGTGATGT 57.149 34.783 0.00 0.00 0.00 3.06
2305 2386 5.590145 TGTTGGAAAATCTTGTGTGATGTG 58.410 37.500 0.00 0.00 0.00 3.21
2306 2387 5.126869 TGTTGGAAAATCTTGTGTGATGTGT 59.873 36.000 0.00 0.00 0.00 3.72
2317 2398 6.815142 TCTTGTGTGATGTGTATCTTGATCTG 59.185 38.462 0.00 0.00 34.31 2.90
2323 2404 5.367644 TGATGTGTATCTTGATCTGTCCCAT 59.632 40.000 0.00 0.00 34.31 4.00
2519 2600 5.946377 AGCCTTTTCCACCTAGATAAACTTG 59.054 40.000 0.00 0.00 0.00 3.16
2819 2902 6.992063 ACATATTTGACTAGCTTGAACCTG 57.008 37.500 1.04 0.00 0.00 4.00
2831 2914 4.397417 AGCTTGAACCTGTCATTCAATAGC 59.603 41.667 2.79 4.19 43.31 2.97
2832 2915 4.156556 GCTTGAACCTGTCATTCAATAGCA 59.843 41.667 2.79 0.00 43.31 3.49
2833 2916 5.675575 GCTTGAACCTGTCATTCAATAGCAG 60.676 44.000 2.79 0.00 43.31 4.24
2901 2984 1.672881 CGCAGTCCTTGATTGGGAATC 59.327 52.381 0.00 0.00 35.02 2.52
2937 3020 1.444836 CCCGCACGTAAGATTTCCAA 58.555 50.000 0.00 0.00 43.62 3.53
3011 3094 5.239525 ACTTCCAACACTCACATTAGCTTTC 59.760 40.000 0.00 0.00 0.00 2.62
3035 3118 4.319261 GGCGCCGTTGTTATTTCCTTATAG 60.319 45.833 12.58 0.00 0.00 1.31
3090 3173 6.766944 AGACATCAAAGCTTCTATTGATCCAG 59.233 38.462 8.14 2.01 42.72 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.975713 GCCTCTGCATTGCATCAAAATGATG 61.976 44.000 12.53 14.46 45.88 3.07
27 28 3.677700 GCCTCTGCATTGCATCAAAATGA 60.678 43.478 12.53 3.14 38.13 2.57
35 36 2.831742 CCGGCCTCTGCATTGCAT 60.832 61.111 12.53 0.00 38.13 3.96
48 49 1.100510 GAAAACAGGATTACCCCGGC 58.899 55.000 0.00 0.00 36.73 6.13
49 50 2.801077 AGAAAACAGGATTACCCCGG 57.199 50.000 0.00 0.00 36.73 5.73
78 80 4.058124 CCGTATAGCAACATATGTGCACT 58.942 43.478 19.41 16.96 0.00 4.40
80 82 4.055360 GTCCGTATAGCAACATATGTGCA 58.945 43.478 23.27 14.18 0.00 4.57
81 83 3.121279 CGTCCGTATAGCAACATATGTGC 59.879 47.826 9.63 14.54 0.00 4.57
84 86 4.542735 TGTCGTCCGTATAGCAACATATG 58.457 43.478 0.00 0.00 0.00 1.78
85 87 4.841443 TGTCGTCCGTATAGCAACATAT 57.159 40.909 0.00 0.00 0.00 1.78
86 88 4.635833 TTGTCGTCCGTATAGCAACATA 57.364 40.909 0.00 0.00 0.00 2.29
87 89 3.513680 TTGTCGTCCGTATAGCAACAT 57.486 42.857 0.00 0.00 0.00 2.71
88 90 3.183754 CATTGTCGTCCGTATAGCAACA 58.816 45.455 0.00 0.00 0.00 3.33
89 91 2.034001 GCATTGTCGTCCGTATAGCAAC 60.034 50.000 0.00 0.00 0.00 4.17
90 92 2.198406 GCATTGTCGTCCGTATAGCAA 58.802 47.619 0.00 0.00 0.00 3.91
91 93 1.847818 GCATTGTCGTCCGTATAGCA 58.152 50.000 0.00 0.00 0.00 3.49
96 98 0.520847 TACACGCATTGTCGTCCGTA 59.479 50.000 3.67 2.85 41.21 4.02
111 113 2.830104 AGTTTCCTGTTCACCGTACAC 58.170 47.619 0.00 0.00 0.00 2.90
138 140 4.980805 TCGCTGCCCGTTCACCAC 62.981 66.667 0.00 0.00 38.35 4.16
139 141 4.680237 CTCGCTGCCCGTTCACCA 62.680 66.667 0.00 0.00 38.35 4.17
176 178 2.267426 CGTTCATTATCACACGGCAGA 58.733 47.619 0.00 0.00 0.00 4.26
182 184 3.002656 CCAGCATCCGTTCATTATCACAC 59.997 47.826 0.00 0.00 0.00 3.82
211 213 1.300481 GCCGCCTTCTAAACCTCATC 58.700 55.000 0.00 0.00 0.00 2.92
241 243 3.000322 CGTCGATCATTAAGTGCAGGAAC 60.000 47.826 0.00 0.00 0.00 3.62
244 246 1.860950 CCGTCGATCATTAAGTGCAGG 59.139 52.381 0.00 0.00 0.00 4.85
264 272 2.670414 CTGTGCAACTAGCTAGACTTGC 59.330 50.000 29.03 29.03 45.94 4.01
266 274 4.310769 CAACTGTGCAACTAGCTAGACTT 58.689 43.478 27.45 9.25 45.94 3.01
273 281 1.266989 GGTTCCAACTGTGCAACTAGC 59.733 52.381 0.00 0.00 45.96 3.42
274 282 2.571212 TGGTTCCAACTGTGCAACTAG 58.429 47.619 0.00 0.00 38.04 2.57
288 296 7.329226 CACAAGTGTATTGATGAATTTGGTTCC 59.671 37.037 0.00 0.00 35.91 3.62
292 300 6.923012 TCCACAAGTGTATTGATGAATTTGG 58.077 36.000 0.00 0.00 0.00 3.28
293 301 8.815141 TTTCCACAAGTGTATTGATGAATTTG 57.185 30.769 0.00 0.00 0.00 2.32
295 303 9.643693 GAATTTCCACAAGTGTATTGATGAATT 57.356 29.630 0.00 0.00 0.00 2.17
296 304 8.253113 GGAATTTCCACAAGTGTATTGATGAAT 58.747 33.333 10.67 0.00 36.28 2.57
297 305 7.232330 TGGAATTTCCACAAGTGTATTGATGAA 59.768 33.333 14.24 0.00 42.67 2.57
298 306 6.718912 TGGAATTTCCACAAGTGTATTGATGA 59.281 34.615 14.24 0.00 42.67 2.92
299 307 6.923012 TGGAATTTCCACAAGTGTATTGATG 58.077 36.000 14.24 0.00 42.67 3.07
345 353 5.664457 TCAAGATACGTGCAGATTTGAGAT 58.336 37.500 0.00 0.00 0.00 2.75
348 356 9.710900 ATATATTCAAGATACGTGCAGATTTGA 57.289 29.630 0.00 0.00 0.00 2.69
378 386 5.005971 TGAAGTGCACAAGTAAACGAAGTAC 59.994 40.000 21.04 0.00 45.00 2.73
393 401 4.858935 TCTAACAAAATGCTGAAGTGCAC 58.141 39.130 9.40 9.40 46.33 4.57
423 431 1.743995 AAGCATAACGACACGGCCC 60.744 57.895 0.00 0.00 0.00 5.80
449 457 1.405463 TGGAAGTCATCACCTCGATCG 59.595 52.381 9.36 9.36 29.21 3.69
453 461 1.945387 CCATGGAAGTCATCACCTCG 58.055 55.000 5.56 0.00 32.92 4.63
487 495 1.950484 GCTTTGCCACTAGCTAGCCAA 60.950 52.381 20.91 17.11 44.23 4.52
489 497 0.107459 AGCTTTGCCACTAGCTAGCC 60.107 55.000 20.91 9.85 45.46 3.93
511 519 4.248402 CGGACGAAAACGCCTACA 57.752 55.556 0.00 0.00 0.00 2.74
543 551 3.068881 CACCACACGTCCAGGGAT 58.931 61.111 0.00 0.00 0.00 3.85
545 553 3.551496 ATGCACCACACGTCCAGGG 62.551 63.158 0.00 0.00 0.00 4.45
571 579 1.797933 CCGAACGAGAGCGACACTG 60.798 63.158 0.00 0.00 41.64 3.66
575 583 0.445436 TTAGTCCGAACGAGAGCGAC 59.555 55.000 0.00 0.00 41.64 5.19
637 687 3.181507 CCACAAGTGCATCGGTCAATTAG 60.182 47.826 0.00 0.00 0.00 1.73
639 689 1.541147 CCACAAGTGCATCGGTCAATT 59.459 47.619 0.00 0.00 0.00 2.32
645 695 2.191354 CTGTGCCACAAGTGCATCGG 62.191 60.000 0.00 0.00 41.46 4.18
666 716 6.393171 GCTTTCTGCACAATCTAATCCTTTT 58.607 36.000 0.00 0.00 42.31 2.27
709 759 2.054021 TGTGGAGTGAACATCAAGGGA 58.946 47.619 0.00 0.00 0.00 4.20
731 802 2.437359 GAGCGGCCATTGAGCTGT 60.437 61.111 6.83 0.00 41.84 4.40
795 869 0.248458 GAGAAGAAGCCGAGAGAGCG 60.248 60.000 0.00 0.00 34.64 5.03
817 891 1.156736 CCATTGTCACTGTTCGGACC 58.843 55.000 0.00 0.00 33.09 4.46
824 898 1.134128 TGTCACTGCCATTGTCACTGT 60.134 47.619 0.00 0.00 0.00 3.55
830 907 1.442769 GTCGATGTCACTGCCATTGT 58.557 50.000 0.00 0.00 0.00 2.71
855 932 0.590195 CTTTGAAAGTGAGCAGCGCT 59.410 50.000 2.64 2.64 43.88 5.92
865 942 0.308993 GCGAGCTGTGCTTTGAAAGT 59.691 50.000 6.81 0.00 39.88 2.66
937 1014 1.673665 ACGAGACGCCGACCTAGTT 60.674 57.895 0.00 0.00 0.00 2.24
1093 1170 3.968649 TGTAACCTACCAAGTTCCACTGA 59.031 43.478 0.00 0.00 0.00 3.41
1148 1225 1.722011 AGGTATGGCGTCAGAAAACG 58.278 50.000 0.00 0.00 45.31 3.60
1530 1611 5.287035 GCTAAAACTTTGATTGCTCGGAATG 59.713 40.000 0.00 0.00 0.00 2.67
1579 1660 5.842339 ACCCTCAAATTTGTTCCCAGATAT 58.158 37.500 17.47 0.00 0.00 1.63
1599 1680 2.502142 ACCCTATTGAAAACCGACCC 57.498 50.000 0.00 0.00 0.00 4.46
1609 1690 5.628797 TGACATGATGCTAACCCTATTGA 57.371 39.130 0.00 0.00 0.00 2.57
1720 1801 7.574607 CCAGTAAGGTTATTAGAACCCAAGAT 58.425 38.462 5.02 0.00 41.18 2.40
1843 1924 9.793259 AAGATTAAGAAACCAGAGTTCATGTAA 57.207 29.630 0.00 0.00 34.19 2.41
1859 1940 8.253113 GCAATTGATTTCTCCCAAGATTAAGAA 58.747 33.333 10.34 0.00 0.00 2.52
1872 1953 9.521503 GGAATTTTACCTAGCAATTGATTTCTC 57.478 33.333 10.34 0.00 0.00 2.87
1875 1956 9.034800 TCAGGAATTTTACCTAGCAATTGATTT 57.965 29.630 10.34 0.00 35.84 2.17
1885 1966 5.452077 CGAGGGAGTCAGGAATTTTACCTAG 60.452 48.000 0.00 0.00 35.84 3.02
1886 1967 4.404715 CGAGGGAGTCAGGAATTTTACCTA 59.595 45.833 0.00 0.00 35.84 3.08
1956 2037 2.969821 TTGTTGGTACTTGGCCAGAT 57.030 45.000 5.11 0.00 37.31 2.90
2130 2211 5.347907 GTCTAATTGTGTACTGAGGTTTCCG 59.652 44.000 0.00 0.00 0.00 4.30
2169 2250 7.224167 GGAAGTCCACCTATTAACTTGTTATCG 59.776 40.741 0.00 0.00 32.34 2.92
2225 2306 5.105064 TGGTTGTGGCTAAGGTCTATTAGAC 60.105 44.000 14.34 14.34 44.32 2.59
2235 2316 3.057315 CAGTGAATTGGTTGTGGCTAAGG 60.057 47.826 0.00 0.00 0.00 2.69
2242 2323 1.270550 GGGCTCAGTGAATTGGTTGTG 59.729 52.381 0.00 0.00 0.00 3.33
2249 2330 2.309755 TCTGGAATGGGCTCAGTGAATT 59.690 45.455 0.00 0.00 0.00 2.17
2278 2359 8.084073 ACATCACACAAGATTTTCCAACATAAG 58.916 33.333 0.00 0.00 0.00 1.73
2300 2381 5.282055 TGGGACAGATCAAGATACACATC 57.718 43.478 0.00 0.00 0.00 3.06
2317 2398 5.044846 AGGGCCTAACATATCATTATGGGAC 60.045 44.000 2.82 0.00 39.69 4.46
2323 2404 7.806680 TGTGATAGGGCCTAACATATCATTA 57.193 36.000 24.14 11.50 37.09 1.90
2819 2902 4.749099 CCTGCTAGACTGCTATTGAATGAC 59.251 45.833 0.00 0.00 0.00 3.06
2831 2914 2.565841 GGTATTTGGCCTGCTAGACTG 58.434 52.381 3.32 0.00 0.00 3.51
2832 2915 1.139058 CGGTATTTGGCCTGCTAGACT 59.861 52.381 3.32 0.00 0.00 3.24
2833 2916 1.583054 CGGTATTTGGCCTGCTAGAC 58.417 55.000 3.32 0.00 0.00 2.59
2863 2946 2.224523 TGCGAGGTGAGGTTTGAGAAAT 60.225 45.455 0.00 0.00 0.00 2.17
2901 2984 1.742768 GGGCTCCACATAGACGAGG 59.257 63.158 0.00 0.00 0.00 4.63
2925 3008 5.106712 TGTCGAAGCATGTTGGAAATCTTAC 60.107 40.000 0.00 0.00 0.00 2.34
2937 3020 3.668447 AGTGAGATTTGTCGAAGCATGT 58.332 40.909 0.00 0.00 0.00 3.21
3011 3094 1.226184 GGAAATAACAACGGCGCCG 60.226 57.895 44.88 44.88 46.03 6.46
3050 3133 7.510549 TTTGATGTCTCCCTTCTTAAGTTTG 57.489 36.000 1.63 0.00 0.00 2.93
3131 3214 6.811170 CACTAAAATTATTGGTGGCGTGAATT 59.189 34.615 8.15 0.00 0.00 2.17
3276 3359 2.645838 AGCACTTGACACTCCACATT 57.354 45.000 0.00 0.00 0.00 2.71


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.